Recent publications

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    1. Chakraborty, S. and Krishnan, Y.* (2017) A structural map of oncomiR-1 at single-nucleotide resolution Nucleic Acids Research, in press
    2. Chakraborty, K., Leung, K., and Krishnan, Y.* (2017) High lumenal chloride in the lysosome is critical for lysosome function. eLife, 6, e28862.
    3. Veetil, A.T., Chakraborty, K.,† Xiao, K.,† Minter, R. M.,† Sisodia, S. S., and Krishnan, Y.* (2017) Cell targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nature Nanotechnology, in press († equal contributions)
    4. Patel, A., Malinovska, L., Saha, S., Wang, J., Alberti, S., Krishnan, Y.* and Hyman, A.A.* (2017) ATP as a biological hydrotrope. Science, 356, 753-756.
    5. Joshi, H., Bhatia, D., Krishnan, Y. and Maiti, P.K.* (2017) Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations Nanoscale, 2017, 9, 4467
    6. Bhatia, D., Arumugam, S., Nasilowski, M., Joshi, H., Wunder, C., Chambon, V., Prakash, V., Grazon, C., Nadal, B., Maiti, P. K., Johannes, L.*, Dubertret, B.* and Krishnan, Y.* (2016) Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nature Nanotechnology, doi:10.1038/nnano.2016.150
    7. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349-373
    8. Prakash, V.,† Saha, S.,† Chakraborty, K. and Krishnan, Y.* (2016) Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chemical Science, 2016, 7, 1946 - 1953, DOI: 10.1039/C5SC04002G († both authors have contributed equally)
    9. Saha, S., Prakash, V., Halder, S., Chakraborty, K. and Krishnan, Y.* (2015) A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells Nature Nanotechnology, 10, 645–651, DOI: 10.1038/NNANO.2015.130.
    10. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
      1. Complete list of Publications

        1. Nucleic acid nano-devices in live imaging
        2. Nucleic acid structure and dynamics
        3. Naturally occurring nucleic acid nano-devices
        4. Reviews and commentaries
        5. Patents
        6. Nucleic acid nano-devices in live imaging

          1. Chakraborty, K., Leung, K., and Krishnan, Y.* (2017) High lumenal chloride in the lysosome is critical for lysosome function. eLife, 6, e28862.
          2. Veetil, A.T., Chakraborty, K.,† Xiao, K.,† Minter, R. M.,† Sisodia, S. S., and Krishnan, Y.* (2017) Cell targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nature Nanotechnology, in press († equal contributions)
          3. Bhatia, D., Arumugam, S., Nasilowski, M., Joshi, H., Wunder, C., Chambon, V., Prakash, V., Grazon, C., Nadal, B., Maiti, P. K., Johannes, L.*, Dubertret, B.* and Krishnan, Y.* (2016) Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nature Nanotechnology, 11, 1112–1119
          4. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349-373
          5. Prakash, V.,† Saha, S.,† Chakraborty, K. and Krishnan, Y.* (2016) Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chemical Science, 2016, 7, 1946-1953. († both authors have contributed equally)
          6. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
          7. Saha, S., Prakash, V., Halder, S., Chakraborty, K. and Krishnan, Y.* (2015) A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells Nature Nanotechnology, 10, 645–651, DOI: 10.1038/NNANO.2015.130.
          8. Banerjee, A., Grazon, C., Nadal, B., Pons, T., Krishnan, Y. and Dubertret, B. * (2015) Fast, efficient and stable conjugation of multiple DNA strands on colloidal quantum dots Bioconjugate Chem., 2015, 10.1021/acs.bioconjchem.5b00221
          9. Modi, S., Halder, S., Nizak, C. and Krishnan, Y.* (2014) Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale, 6, 1144-1152.
          10. Ganesh, K.N. and Krishnan Y. (2013) Nucleic Acids - Chemistry and Applications. J. Org. Chem. 78, 12283-12287.
          11. Modi, S., Nizak, C., Surana, S., Halder, S. and Krishnan, Y*. (2013)Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nature Nanotechnology, 8, 459-467.
          12. Surana, S., Bhatia, D. and Krishnan, Y.* (2013) A method to study in vivo stability of DNA nanostructures. Methods, 64, 94-100.
          13. Surana, S. and Krishnan, Y.* (2013) A method to map spatiotemporal pH changes in a multicellular living organism using a DNA nanosensor. Methods Mol. Biol. 991, 9-23.
          14. Krishnan, Y.*, Bathe, M.* (2012) Designer nucleic acids to probe and program the cell.Trends in Cell Biology, 22, 624-633.
          15. Modi, S. and Krishnan, Y.* (2011) A method to map spatiotemporal pH changes insde living cells using a pH triggered DNA nanoswitch. Methods Mol. Biol. 749, 61-77.
          16. Surana, S., Bhat, J.M., Koushika, S.P. and Krishnan, Y.* (2011) An autonomous DNA nanomachine maps spatiotemporal pH changes in a molticellolar living organism.Nature Communications, 2, 340.
          17. Bhatia, D., Surana, S., Chakraborty, S., Koushika, S.P. and Krishnan, Y.* (2011) A synthetic, icosahedral DNA-based host-cargo complex for functional in vivo imaging.Nature Communications, 2, 339.
          18. Modi, S., Swetha, M. G., Goswami, D., Gupta, G. D., Mayor, S., Krishnan, Y.* (2009) A DNA nanomachine maps spatiotemporal pH changes in living cells. Nature Nanotechnology, 4, 325-330.

        Nucleic acid structure and dynamics

        1. Patel, A., Malinovska, L., Saha, S., Wang, J., Alberti, S., Krishnan, Y.* and Hyman, A.A.* (2017) ATP as a biological hydrotrope. Science, 356, 753-756.
        2. Joshi, H., Bhatia, D., Krishnan, Y. and Maiti, P.K.* (2017) Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations Nanoscale, 9, 4467
        3. Halder, S. and Krishnan, Y.* (2015) Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. Nanoscale, 2015, 7, 10008-10012.
        4. Lannes, L., Halder, S., Krishnan, Y. and Schwalbe, H.* (2015) Tuning the pH Response of i-Motif DNA Oligonucleotides ChemBioChem, 2015, 10.1002/cbic.201500182.
        5. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710-1719.
        6. Sharma, S., Zaveri, A., Visweswariah, S.S and Krishnan, Y.* (2014) A fluorescent nucleic acid-based nanodevice quantitatively images elevated cAMP in membrane bound compartments. Small, 10, 4276–4280.
        7. Banerjee, A., Bhatia, D., Saminathan, A., Chakraborty, S., Kar, S. and Krishnan, Y.* (2013) Controlled release of encapsulated cargo from a DNA icosahedron using a chemical trigger. Angew. Chem. Int. Ed. 52, 6854-6857.
        8. Bhatia, D., Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2013) A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol. Biol. 991, 65-80.
        9. Bhatia, D. and Krishnan, Y. (2013) Designer nucleic acid-based devices in nanomedicine. In Erdmann, V.A., Barcisjewski, J. (eds), DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases. pp 1-10.
        10. Saha, S. and Krishnan, Y. (2012) pH sensitive DNA devices. In Fox, K.R., Brown, T (ed), DNA Conjugates and Sensors. Royal Society of Chemistry publishing, Cambridge, pp166-183.
        11. Saha, S., Chakraborty, K. and Krishnan, Y*. (2012) Tunable, colorimetric DNA based pH sensors mediated by A-motif formation. Chem. Commun. 48, 2513.
        12. Bhatia, D., Sharma, S. and Krishnan, Y*. (2011) Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol, 22, 475-484.
        13. Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based Molecular Devices. Angew. Chem. Int. Ed. 50, 3124-3156.
        14. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* (2010) Structural DNA Nanotechnology: From bases to bricks, from structure to function. J. Phys. Chem. Lett. 1, 1999-2005.
        15. Saha, S., Bhatia, D., Krishnan, Y.* (2010) pH toggled DNA architectures: Reversible assembly of a 3WJ into extended 1D architectures through A-motif formation . Small, 6, 1288-1292.
        16. Chakraborty, S., Sharma, S., Maiti, P. K., Krishnan, Y.* (2009) The poly dA helix: A new structural motif for high-performance DNA-based molecular switches . Nucleic Acids Res. 37, 2810-2817.
        17. Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A., Krishnan, Y.*(2009)Icosahedral DNA nanocapsules via modular assembly. Angew. Chem. Int. Ed. 48, 4134-4137. (featured on journal frontispiece)
        18. Paol,  A.; Sengupta, P.;  Krishnan, Y.; Ladame, S.* (2008) Combining G-quadruplex targeting motifs on a single PNA scaffold: hybrid (3+1) PNA-DNA bimolecular quadruplex. Chem.Eur.J. 14, 8682-8689.
        19. Chakraborty, S.; Krishnan, Y.* (2008) Kinetic Hybrid i-motifs: Intercepting DNA with RNA to form a DNA2-RNA2 i-motif. Biochimie, 90, 1088-1095.
        20. Chakraborty, S.; Modi, S.; Krishnan, Y.* (2008) The RNA2-PNA2 Hybrid I-motif - A novel RNA-based building block. Chem. Commun., 70-72.
        21. Ghodke, H. B.; Krishnan, R.; Vignesh, K.; Kumar, G.V.P.; Narayana, C.; Krishnan, Y.* (2007) The I-tetraplex building block: Rational Design and Controlled Fabrication of robust 1D DNA Scaffolds via non-Watson Crick self assembly. Angew. Chem. Int. Ed., 46, 2646-2649.
        22. Gavory, G.; Symmons, M. F.; Krishnan-Ghosh, Y.;Klenerman, D.; Balasubramanian, S.* (2006) Structural Analysis of the Catalytic Core of Human Telomerase RNA by FRETand Molecolar Modeling. Biochemistry, 45, 13304-13311.
        23. Modi, S., Wani, A. H., Krishnan, Y.* (2006) The PNA-DNA hybrid I-motif - Implications for sugar-sugar contacts in i-motif tetramerization. Nucleic Acids Research, 34, 4353-4363.
        24. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.*(2005) PNA forms an I-motif. Chem. Commun. 5278-5280.
        25. Krishnan-Ghosh, Y.; Whitney, A. M.; Balasubramanian, S.* (2005)  Dynamic covalent chemistry on self-templating PNA oligomers: Formation of a bimolecolar PNA quadruplex. Chem. Commun., 3068-3070.
        26. Krishnan-Ghosh, Y.; Liu, D.; Balasubramanian, S.* (2004) Formation of an interlocked quadruplex dimer by d(GGGT). J. Am. Chem. Soc. 126, 11009-11016.
        27. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* (2004)A PNA4 quadruplex.  J. Am. Chem. Soc.  126, 5944-5945.
        28. Krishnan-Ghosh , Y.; Balasubramanian, S.* (2003) Dynamic covalent chemistry on self-templating peptides: Formation of a disolfide-linked beta-hairpin mimic. Angew. Chem. Int. Ed. 42, 2171-2173.
        29. Ghosh Y. K.; Visweswariah, S. S.; Bhattacharya, S. * (2002) Advantage of the ether linkage between the positive charge and the cholesteryl skeleton in cholesterol-based amphiphiles as vectors for gene delivery. Bioconjugate Chem. 13, 378-384. 
        30. Bhattacharya, S.*; Krishnan-Ghosh, Y. (2002) 2-Halooxyethylene ethers of cholesterol as novel single component, room temperature cholesteric LC materials.Mol. Cryst. Liq. Cryst. 381, 33-41. 
        31. Wills, A. J.; Krishnan-Ghosh, Y.; Balasubramanian S.* (2002) Synthesis of a polymer-supported oxazolidine aldehyde for asymmetric chemistry. J. Org. Chem. 67, 6646-6652.
        32. Horsey, I.; Krishnan-Ghosh, Y.; Balasubramanian, S. (2002) Enhanced cooperative binding of oligonucleotides to form DNA duplexes mediated by metal ion chelation Chem. Commun. 1950-1951. 
        33. Bhattacharya, S.; Krishnan-Ghosh, Y. (2001) First report of phase selective gelation of oil from oil/water mixtures. Possible implications toward containing oil spills. Chem. Commun., 185-186.
        34. Bhattacharya, S.; Krishnan-Ghosh, Y. (2001) Vesicle formation from oligo(oxyethylene)-bearing cholesteryl amphiphiles: Site-selective effects of oxyethylene units on the membrane order and thickness. Langmuir 17, 2067-2075.
        35. Krishnan-Ghosh, Y.; Gopalan, R. S.; Kolkarni, G. U.; Bhattacharya, S. (2001) Structure of cholest-5-en-3 beta-oxy-5-bromopentane by single-crystal X-ray diffraction at 130 K. J. Mol. Structure 560, 345-355. 
        36. Krishnan-Ghosh, Y.; Bhattacharya, S.* (2001) Membrane formation from oxyethylene bearing cationic cholesterol derivatives. Ind. J. Chem. B. 40, 891-894.
        37. Krishnan-Ghosh, Y., Bhattacharya, S.* (2001) Thermal lipid order-disorder transitions in mixtures of cationic cholesteryl lipid analogues and dipalmitoyl phosphatidylcholine membranes. J. Phys. Chem. B. 105, 10257-10265.
        38. Ghosh, Y.K., Visweswariah, S. S., Bhattacharya, S.* (2000) Nature of linkage between cationic headgroup and cholesteryl skeleton controls gene transfection efficiency .  FEBS Lett. 473, 341-344

        Naturally occurring nucleic acid nano-devices

        1. Chakraborty, S. and Krishnan, Y.* (2017) A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Research, in press
        2. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710-1719.
        3. Chakraborty, S., Mehtab, S., Patwardhan, A.R., Krishnan, Y.* (2012) Pri-miR-17-92a Transcript folds into a tertiary structure and autoregolates its processing. RNA 18, 1014-1028.

        Reviews and commentaries:

        1. Voices of biotech   Nature Biotechnology, 34, (2016),  270–275
        2. Nature nanotechnology 10 the anniversary issue opinion piece  Nature Nanotechnology (2016) 11,  828–834
        3. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349-373
        4. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
        5. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710-1719.
        6. Ghosh, A. and Krishnan, Y. (2014) At a long-awaited turning point. NatureNanotechnology, 9, 491-494.
        7. Krishnan, Y., Bathe, M. (2012) Designer nucleic acids to probe and program the cell.Trends in Cell Biology, 22, 624-633.
        8. Bhatia, D., Chakraborty, S. and Krishnan, Y.* (2012) Designer DNA give RNAi more spine. Nature Nanotechnology, 7, 344-346.
        9. Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based Molecolar Devices. Angew. Chem. Int. Ed. 50, 3124-3156.
        10. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* (2010) Structural DNA Nanotechnology: From bases to bricks, from structure to function. J.Phys. Chem. Lett. 1, 1999-2005.
        11. Pitchiaya, S., Krishnan, Y.* (2006) First Blueprint, Now Bricks: DNA as construction material on the nanoscale. Chem. Soc. Rev., 35, 1111-1121.

        Patents:

        1. Modular assembly of novel icosahedral DNA nanocapsules with encapsulating ability.

          Yamuna Krishnan. Under prosecution at USPTO.

        2. The A-motif: A pH trigger for hybridization of DNA strands

          Saikat Chakraborty and Yamuna Krishnan.
          US Patent granted July 10, 2012. USPTO no: 8216850.

        3. FRET based pH Sensor using nucleic acid assemblies.

          Yamuna Krishnan, Satyajit Mayor and Souvik Modi. Under prosecution at USPTO.

        4. An engineered nucleic acid assembly, vector, cell, methods and kit thereof

          Souvik Modi and Yamuna Krishnan. Complete IN and PCT filed.

        5. A process for encapsulating functional biomolecules and encapsulated product thereof.

          Dhiraj Bhatia and Yamuna Krishnan. Complete IN and PCT filed.
          Winner of the Amulya 2012 award from the Karnataka State Innovation Council.

        6. Nucleotide sequences, nucleic acid sensors and methods thereof.

          Suruchi Sharma and Yamuna Krishnan. Complete IN filed.

        7. Nucleic Acids based sensor and methods thereof.

          Sonali Saha and Yamuna Krishnan. Complete IN filed.

        8. A process for encapsulating functional biomolecules and encapsulated product thereof.

          Souvik Modi, Sunaina Surana and Yamuna Krishnan. PCT filed. PCT/IB/2014/059236